Chromatin States in Pancreatic Ductal Adenocarcinoma Control Metastatic Spread

By Stuart P. Atkinson

Restoring Smad4 was tested across different tumor‑seeding experiments (pancreas, liver and lung) and produced striking, organ‑specific results: it had little effect on the primary pancreatic mass, strongly reduced liver metastases, and unexpectedly increased lung metastases — findings measured by imaging and lesion counts. This contrast motivates the paper’s main question: why does the same genetic change drive opposite outcomes in different organs? The figure summarizes those experiments and their readouts, setting up the study’s deeper analysis of how early chromatin states shape where pancreatic tumors spread. Adapted from Fig. 2 of Tsanov et al.

Chromatin States in Pancreatic Ductal Adenocarcinoma Control Metastatic Spread

Smad4 turns on genes that slow tumor growth in the liver but turns on different genes that promote growth in the lung. Adapted from Fig. 3 of Tsanov et al.

What Drives Metastasis in Pancreatic Ductal Adenocarcinoma Patients?

Mutations that inactivate the SMAD4 tumor suppressor gene, a core mediator of the transforming growth factor-β (TGF-β) signaling pathway, represent a hallmark of pancreatic ductal adenocarcinoma (PDAC) (Nguyen et al. and Hoadley et al.).SMAD4 inactivation during cancer progression supports the tumor-promoting activity of the TGF-β pathway (Massague & Sheppard), and SMAD4-mutant tumors have higher rates of metastasis in PDAC patients (Blackford et al.) however, the impact of tumorigenesis-associated mutations on metastasis remains poorly understood. Indeed, while we possess an in-depth understanding of the alterations that a tumor cell requires to metastasize (Birkbak & McGranahan and Turajlic & Swanton), we know only a few metastatic tumor-specific driver gene mutations (Reiter et al., Priestley et al., and Nguyen et al.), which suggests that pro-metastatic traits arise from epigenetic programs that facilitate cell state changes. Given that metastasis accounts for 90% of cancer-related deaths (Lambert, Pattabiraman, & Weinberg), that most PDAC patients present with metastasis (Kleeff et al.), and that we currently lack effective strategies to target the TGF-β pathway or metastasis in general, additional knowledge in this area remains vital.

To determine the dependence of metastatic tumors on SMAD4 inactivation, researchers led by Kaloyan M. Tsanov (University of Chicago) and Scott W. Lowe (Memorial Sloan Kettering Cancer Center) developed a mouse model of PDAC that enables inducible, reversible Smad4 inactivation at different stages of PDAC progression. Their new Nature Cancer study now reveals that Smad4 reactivation in metastatic PDAC cells suppresses liver metastases but promotes lung metastases thanks to organ-specific chromatin states that emerge in premalignant pancreatic tissues (Tsanov et al.). Could these findings have significant implications for interpreting tumor genetics and treating PDAC metastasis?

Paired-Tag technology from Epigenome Technologies enables the simultaneous profiling of transcriptomics and epigenetics in single cells; could the integration of this approach as part of this fascinating new study have yielded additional insights into how driver mutations impact metastasis, the role of tumor cell chromatin states, and potentially targetable pathways that could help to treat this invariably deadly stage of cancer progression? Paired-Tag technology from Epigenome Technologies generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with comparable efficiency to single-nucleus RNA-seq/ChIP-seq assays while avoiding the need for cell sorting.

Single‑cell profiles show that, early in tumor development, distinct cell groups already carry liver‑like or lung‑like chromatin patterns that bias where tumors spread. Adapted from Fig. 6 of Tsanov et al.

Distinct Chromatin States Mediate Site-Specific Smad4 Reactivation-induced Metastasis

Studying Smad4 reactivation in metastatic tumors employed transplantation assays using prometastatic cell lines derived from primary tumors in genetically engineered mouse models. Interestingly,Smad4 inactivation promoted liver metastases and inhibited lung metastases, a finding that agreed with SMAD4 protein expression patterns in human metastatic PDAC patients. Subsequent RNA-sequencing analysis revealed a distinct Smad4-associated transcriptional profile in the liver versus the lung; overall, the authors highlighted a Smad4-induced tumor-suppressive gene expression profile in the liver and a tumor-promoting gene expression profile in the lung.

The authors hypothesized that liver and lung metastases from primary PDAC tumors may harbor distinct chromatin states that afford different accessibility to Smad4 target genes, given the observed organ-specific transcriptional responses. Interestingly, ATAC-seq (assay for transposase-accessible chromatin using sequencing) revealed that dissemination to the liver versus the lungs favors distinct chromatin states in tumor cells, in which certain transcription factor activities are stably inherited and associated with opposite dependence on Smad4 inactivation. Subsequent single-cell multiomics analyses (scATAC-seq + scRNA-seq) to investigate the presence of heritable organ-associated epigenetic programs in the primary PDAC tumor revealed that the liver and lungs favor metastatic cells harboring distinct chromatin states that emerge in distinct subpopulations of the premalignant pancreas. Furthermore, these chromatin states were differentially favored by Smad4 status and tissue injury and maintained in primary tumors.

The authors finally integrated ATAC-seq and RNA-seq datasets to identify transcription factor families with motifs enriched in differentially accessible chromatin regions and upregulated predicted targets upon Smad4 reactivation. These analyses provided evidence that the Klf4 and Runx1 mediated organ-specific chromatin opening and differential dependence on Smad4 inactivation in liver versus lung metastases. Interestingly, Klf4 and Runx1 depletion reversed or dampened Smad4 function in liver and lung metastases, demonstrating that Klf4 facilitates the tumor-suppressive activity of Smad4 in the liver, while Runx1 contributes to the tumor-promoting activity of Smad4 in the lungs.

Combined chromatin and gene‑expression analyses link KLF4 activity with liver‑biased tumor states and RUNX1 activity with lung‑biased states in mouse and human PDAC samples. Adapted from Fig. 7 of Tsanov et al.

Mutation-Chromatin Interplay in Metastasis: The Next Steps for Pancreatic Ductal Adenocarcinoma?

Overall, these findings reveal how gene mutations, such as those that inactivate Smad4, drive metastasis to specific organs depending on the epigenetic state of the cancer cell, with significant implications for tumor genetic interpretation and metastasis treatment. The finding that mutations synergize or antagonize with distinct chromatin states emerging early during tumorigenesis aligns with recent studies highlighting the emergence of prometastatic epigenetic programs in premalignant tissues (Alonso-Curbelo et al. and LaFave et al.) and the ability to predict metastatic sites from transcriptional signatures in primary tumors (Link et al.). The authors suggest that future studies should determine the extent to which organ-specific effects apply to additional cancer driver mutations (e.g.,TP53, KRAS, MYC, and CDKN2A), incorporate cell-type-specific lineage-tracing tools to identify PDAC precursor cell populations with distinct chromatin states that may give rise to the differences in metastatic potential, and define the contribution of additional organ-specific microenvironmental factors to the interplay between gene mutations and chromatin states.

The additional integration of simultaneous profiling of transcriptomics and epigenetics in single cells, afforded by applying Paired-Tag technology from Epigenome Technologies, could provide a more detailed description of the interplay between chromatin states and driver gene mutations in metastatic PDAC (and help to define chromatin states in distinct PDAC precursor cell populations) and thereby help to interpret tumor genetics and treat PDAC metastasis.